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USAMRIID-Led Study Looks at Ebola Transmission, Adaptation in Liberia

NEW YORK (GenomeWeb) – A study appearing online today in Cell Host & Microbe suggests most Liberian Ebola virus infections can be traced back to a form of the virus transmitted from Sierra Leone.

Researchers from the US Army Medical Research Institute of Infectious Diseases and elsewhere did whole-genome sequencing on 140 Ebola virus isolates collected during a second wave of Ebola virus outbreak in Liberia, which began around May 2014.

Comparisons with nearly 800 other isolates collected in Liberia and other parts of West Africa since 2013 pointed to multiple Ebola virus introductions to Liberia. Even so, their results suggested viruses from one lineage in particular were behind most Ebola virus cases in that country.

"This expanded dataset really allowed us to get a clear look at the introductions and spread of the virus," co-first author Jason Ladner, a researcher with USAMRIID's Center for Genome Sciences, told GenomeWeb.

The first wave of Ebola virus infections hit Liberia in around March of 2014, he and his co-authors noted. But that outbreak is believed to have been quite small, involving fewer than 20 confirmed cases. A second stage of the outbreak has been far deadlier — claiming some 4,800 lives and infecting more than 5,800 others since May 2014.

"[R]elatively few sequences have been determined from patients in Liberia, even though this country had the highest number of Ebola-related deaths," USAMRIID's Gustavo Palacios, senior author on the study, said in a statement.

Building on USAMRIID's presence in Liberia during the outbreak and relationships with researchers in the region, Ladner, Palacios, and colleagues tapped into patient samples from the Liberian Institute for Biomedical Research, identifying almost 400 samples that were positive for Ebola virus DNA as determined by real-time PCR testing.

The researchers successfully sequenced 165 of these Ebola virus isolates — a set that included improved sequences for 25 Ebola virus isolates described in an Emerging Infectious Diseases paper earlier this year and 140 newly sequenced isolates from 139 patients infected in Liberia between June 2014 and mid-February of the following year.

A subset of the samples were sequenced at the center in Liberia using an Illumina MiSeq instrument sent over during the outbreak, while other prepared libraries were sent to the US for sequencing on Illumina instruments at USAMRIID.

The mean coverage came in at close to 99 percent of the Ebola virus genome, the team noted, though the coverage for individual isolates was 67.6 percent to 99.7 percent.

For their analyses, the researchers compared these Liberian isolates to sequences for 23 Liberian isolates sequenced by the European Mobile Laboratory or the US Centers for Disease Control and Prevention and 734 sequenced isolates from Guinea, Mali, and Sierra Leone.

Phylogenetic patterns in these samples pointed to the presence of Ebola viruses from multiple transmission sources early on in the outbreak, but the bulk of the cases in Liberia appeared to involve Ebola viruses from the so-called SL2 lineage that are believed to have been introduced to the country from Sierra Leone in late May or early June of 2014.

In contrast, two earlier transmission chains involving viruses from the GM1 and SL1 lineages in Liberia appear to have fizzled out, the team reported.

Ebola viruses from the SL2 lineage contained just a few substitutions — all but one of them synonymous — relative to the shared ancestor of SL1 and SL2 lineage viruses, Ladner noted, arguing against the notion that viruses in the second wave of Liberia infections were especially fit.  

Rather, the study's authors saw clues that the SL2 lineage may have taken hold in Liberia through introductions to high-density neighborhoods such as those in and around the capital city of Monrovia.

"Approximately 70 [percent] of Liberia's reported cases occurred in this region," they wrote, "and it served as an important source of new infections in other parts of the country."

The strain appears to have diversified to some extent in Liberia before being transmitted to individuals in Guinea and Mali.

This diversification did not seem to increase virulence or further adaptation to humans. But it did lead to a sub-lineage of Ebola viruses dubbed LB5 that could be tracked beyond Liberia's borders based on the presence of a characteristic truncation in one of the virus' genes.

Although new Ebola virus infections are now waning in West Africa, those involved in the study cautioned that ongoing surveillance is needed to be sure the virus does not re-emerge, particularly given recent evidence that the virus can be transmitted in semen from survivors showing no further sign of infection.

"People are just starting to explore and understand how long a person can be persistently infected and how long they may be able to pass that virus on to other people," Ladner said.